forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Font;
  31 import java.awt.event.ActionEvent;
  32 import java.awt.event.ComponentAdapter;
  33 import java.awt.event.ComponentEvent;
  34 import java.awt.event.WindowAdapter;
  35 import java.awt.event.WindowEvent;
  36 import java.io.File;
  37 import java.io.FileInputStream;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.net.MalformedURLException;
  41 import java.net.URL;
  42 import java.util.ArrayList;
  43 import java.util.HashSet;
  44 import java.util.List;
  45 import java.util.Set;
  46
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.JCheckBoxMenuItem;
  49 import javax.swing.JFileChooser;
  50 import javax.swing.JMenu;
  51 import javax.swing.JMenuBar;
  52 import javax.swing.JMenuItem;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JRadioButtonMenuItem;
  55 import javax.swing.UIManager;
  56 import javax.swing.UnsupportedLookAndFeelException;
  57 import javax.swing.WindowConstants;
  58 import javax.swing.event.ChangeEvent;
  59 import javax.swing.event.ChangeListener;
  60
  61 import org.forester.analysis.TaxonomyDataManager;
  62 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  63 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
  64 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
  65 import org.forester.archaeopteryx.tools.InferenceManager;
  66 import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
  67 import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
  68 import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
  69 import org.forester.archaeopteryx.tools.SequenceDataRetriver;
  70 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  71 import org.forester.archaeopteryx.webservices.WebservicesManager;
  72 import org.forester.io.parsers.FastaParser;
  73 import org.forester.io.parsers.GeneralMsaParser;
  74 import org.forester.io.parsers.PhylogenyParser;
  75 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  76 import org.forester.io.parsers.nhx.NHXParser;
  77 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  78 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  79 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  80 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  81 import org.forester.io.parsers.tol.TolParser;
  82 import org.forester.io.parsers.util.ParserUtils;
  83 import org.forester.io.writers.SequenceWriter;
  84 import org.forester.msa.Msa;
  85 import org.forester.msa.MsaFormatException;
  86 import org.forester.phylogeny.Phylogeny;
  87 import org.forester.phylogeny.PhylogenyMethods;
  88 import org.forester.phylogeny.PhylogenyNode;
  89 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  90 import org.forester.phylogeny.data.Confidence;
  91 import org.forester.phylogeny.data.PhylogenyDataUtil;
  92 import org.forester.phylogeny.data.Sequence;
  93 import org.forester.phylogeny.data.Taxonomy;
  94 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  95 import org.forester.phylogeny.factories.PhylogenyFactory;
  96 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  97 import org.forester.sequence.MolecularSequence;
  98 import org.forester.util.BasicDescriptiveStatistics;
  99 import org.forester.util.BasicTable;
 100 import org.forester.util.BasicTableParser;
 101 import org.forester.util.DescriptiveStatistics;
 102 import org.forester.util.ForesterUtil;
 103
 104 public final class MainFrameApplication extends MainFrame {
 105
 106     private final static int             FRAME_X_SIZE                    = 800;
 107     private final static int             FRAME_Y_SIZE                    = 800;
 108     // Filters for the file-open dialog (classes defined in this file)
 109     private static final long            serialVersionUID                = -799735726778865234L;
 110     private static final boolean         PREPROCESS_TREES                = false;
 111     private final JFileChooser           _values_filechooser;
 112     private final JFileChooser           _sequences_filechooser;
 113     private final JFileChooser           _open_filechooser;
 114     private final JFileChooser           _msa_filechooser;
 115     private final JFileChooser           _seqs_pi_filechooser;
 116     private final JFileChooser           _open_filechooser_for_species_tree;
 117     // Application-only print menu items
 118     private JMenuItem                    _collapse_below_threshold;
 119     private JMenuItem                    _collapse_below_branch_length;
 120     private ButtonGroup                  _radio_group_1;
 121     private ButtonGroup                  _radio_group_2;
 122     // Others:
 123     double                               _min_not_collapse               = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;
 124     double                               _min_not_collapse_bl            = 0.001;
 125     // Phylogeny Inference menu
 126     private JMenu                        _inference_menu;
 127     private JMenuItem                    _inference_from_msa_item;
 128     private JMenuItem                    _inference_from_seqs_item;
 129     // Phylogeny Inference
 130     private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
 131     private Msa                          _msa                            = null;
 132     private File                         _msa_file                       = null;
 133     private List<MolecularSequence>      _seqs                           = null;
 134     private File                         _seqs_file                      = null;
 135     JMenuItem                            _read_values_jmi;
 136     JMenuItem                            _read_seqs_jmi;
 137
 138     private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
 139         _configuration = config;
 140         if ( _configuration == null ) {
 141             throw new IllegalArgumentException( "configuration is null" );
 142         }
 143         setVisible( false );
 144         setOptions( Options.createInstance( _configuration ) );
 145         _mainpanel = new MainPanel( _configuration, this );
 146         _open_filechooser = null;
 147         _open_filechooser_for_species_tree = null;
 148         _save_filechooser = null;
 149         _writetopdf_filechooser = null;
 150         _writetographics_filechooser = null;
 151         _msa_filechooser = null;
 152         _seqs_pi_filechooser = null;
 153         _values_filechooser = null;
 154         _sequences_filechooser = null;
 155         _jmenubar = new JMenuBar();
 156         buildFileMenu();
 157         buildTypeMenu();
 158         _contentpane = getContentPane();
 159         _contentpane.setLayout( new BorderLayout() );
 160         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 161         // App is this big
 162         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 163         // The window listener
 164         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 165         addWindowListener( new WindowAdapter() {
 166
 167             @Override
 168             public void windowClosing( final WindowEvent e ) {
 169                 exit();
 170             }
 171         } );
 172         //   setVisible( true );
 173         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 174             AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
 175             validate();
 176             getMainPanel().getControlPanel().showWholeAll();
 177             getMainPanel().getControlPanel().showWhole();
 178         }
 179         //activateSaveAllIfNeeded();
 180         // ...and its children
 181         _contentpane.repaint();
 182     }
 183
 184     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
 185         this( phys, config, title, null );
 186     }
 187
 188     private MainFrameApplication( final Phylogeny[] phys,
 189                                   final Configuration config,
 190                                   final String title,
 191                                   final File current_dir ) {
 192         super();
 193         _configuration = config;
 194         if ( _configuration == null ) {
 195             throw new IllegalArgumentException( "configuration is null" );
 196         }
 197         try {
 198             if ( _configuration.isUseNativeUI() ) {
 199                 UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
 200             }
 201             else {
 202                 UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
 203             }
 204         }
 205         catch ( final UnsupportedLookAndFeelException e ) {
 206             AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
 207         }
 208         catch ( final ClassNotFoundException e ) {
 209             AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
 210         }
 211         catch ( final InstantiationException e ) {
 212             AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
 213         }
 214         catch ( final IllegalAccessException e ) {
 215             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
 216         }
 217         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
 218             setCurrentDir( current_dir );
 219         }
 220         // hide until everything is ready
 221         setVisible( false );
 222         setOptions( Options.createInstance( _configuration ) );
 223         setInferenceManager( InferenceManager.createInstance( _configuration ) );
 224         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
 225         // set title
 226         setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );
 227         _mainpanel = new MainPanel( _configuration, this );
 228         // The file dialogs
 229         _open_filechooser = new JFileChooser();
 230         _open_filechooser.setMultiSelectionEnabled( true );
 231         _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );
 232         _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );
 233         _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
 234         _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
 235         _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );
 236         _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );
 237         _open_filechooser.setFileFilter( MainFrame.defaultfilter );
 238         _open_filechooser_for_species_tree = new JFileChooser();
 239         _open_filechooser_for_species_tree.setMultiSelectionEnabled( false );
 240         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );
 241         _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );
 242         _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );
 243         // Msa:
 244         _msa_filechooser = new JFileChooser();
 245         _msa_filechooser.setName( "Read Multiple Sequence Alignment File" );
 246         _msa_filechooser.setMultiSelectionEnabled( false );
 247         _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );
 248         _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );
 249         // Seqs:
 250         _seqs_pi_filechooser = new JFileChooser();
 251         _seqs_pi_filechooser.setName( "Read Sequences File" );
 252         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 253         _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );
 254         _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );
 255         // Expression
 256         _values_filechooser = new JFileChooser();
 257         _values_filechooser.setMultiSelectionEnabled( false );
 258         // Sequences
 259         _sequences_filechooser = new JFileChooser();
 260         _sequences_filechooser.setMultiSelectionEnabled( false );
 261         try {
 262             final String home_dir = System.getProperty( "user.home" );
 263             _open_filechooser.setCurrentDirectory( new File( home_dir ) );
 264             _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) );
 265             _msa_filechooser.setCurrentDirectory( new File( home_dir ) );
 266             _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) );
 267             _values_filechooser.setCurrentDirectory( new File( home_dir ) );
 268             _sequences_filechooser.setCurrentDirectory( new File( home_dir ) );
 269         }
 270         catch ( final Exception e ) {
 271             e.printStackTrace();
 272             // Do nothing. Not important.
 273         }
 274         // build the menu bar
 275         _jmenubar = new JMenuBar();
 276         if ( !_configuration.isUseNativeUI() ) {
 277             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
 278         }
 279         buildFileMenu();
 280         if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {
 281             buildPhylogeneticInferenceMenu();
 282         }
 283         buildAnalysisMenu();
 284         buildToolsMenu();
 285         buildViewMenu();
 286         buildFontSizeMenu();
 287         buildOptionsMenu();
 288         buildTypeMenu();
 289         buildHelpMenu();
 290         setJMenuBar( _jmenubar );
 291         _jmenubar.add( _help_jmenu );
 292         _contentpane = getContentPane();
 293         _contentpane.setLayout( new BorderLayout() );
 294         _contentpane.add( _mainpanel, BorderLayout.CENTER );
 295         // App is this big
 296         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
 297         //        addWindowFocusListener( new WindowAdapter() {
 298         //
 299         //            @Override
 300         //            public void windowGainedFocus( WindowEvent e ) {
 301         //                requestFocusInWindow();
 302         //            }
 303         //        } );
 304         // The window listener
 305         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 306         addWindowListener( new WindowAdapter() {
 307
 308             @Override
 309             public void windowClosing( final WindowEvent e ) {
 310                 if ( isUnsavedDataPresent() ) {
 311                     final int r = JOptionPane.showConfirmDialog( null,
 312                                                                  "Exit despite potentially unsaved changes?",
 313                                                                  "Exit?",
 314                                                                  JOptionPane.YES_NO_OPTION );
 315                     if ( r != JOptionPane.YES_OPTION ) {
 316                         return;
 317                     }
 318                 }
 319                 else {
 320                     final int r = JOptionPane
 321                             .showConfirmDialog( null, "Exit Archaeopteryx?", "Exit?", JOptionPane.YES_NO_OPTION );
 322                     if ( r != JOptionPane.YES_OPTION ) {
 323                         return;
 324                     }
 325                 }
 326                 exit();
 327             }
 328         } );
 329         // The component listener
 330         addComponentListener( new ComponentAdapter() {
 331
 332             @Override
 333             public void componentResized( final ComponentEvent e ) {
 334                 if ( _mainpanel.getCurrentTreePanel() != null ) {
 335                     _mainpanel.getCurrentTreePanel()
 336                             .calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
 337                                                         _mainpanel.getCurrentTreePanel().getHeight() );
 338                 }
 339             }
 340         } );
 341         requestFocusInWindow();
 342         // addKeyListener( this );
 343         setVisible( true );
 344         if ( ( phys != null ) && ( phys.length > 0 ) ) {
 345             AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
 346             validate();
 347             getMainPanel().getControlPanel().showWholeAll();
 348             getMainPanel().getControlPanel().showWhole();
 349         }
 350         activateSaveAllIfNeeded();
 351         // ...and its children
 352         _contentpane.repaint();
 353         System.gc();
 354     }
 355
 356     private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
 357         // Reads the config file (false, false => not url, not applet):
 358         this( phys, new Configuration( config_file, false, false, true ), title );
 359     }
 360
 361     @Override
 362     public void actionPerformed( final ActionEvent e ) {
 363         try {
 364             super.actionPerformed( e );
 365             final Object o = e.getSource();
 366             // Handle app-specific actions here:
 367             if ( o == _open_item ) {
 368                 readPhylogeniesFromFile();
 369             }
 370             if ( o == _open_url_item ) {
 371                 readPhylogeniesFromURL();
 372             }
 373             else if ( o == _new_item ) {
 374                 newTree();
 375             }
 376             else if ( o == _close_item ) {
 377                 closeCurrentPane();
 378             }
 379             else if ( o == _load_species_tree_item ) {
 380                 readSpeciesTreeFromFile();
 381             }
 382             else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
 383                 if ( isSubtreeDisplayed() ) {
 384                     return;
 385                 }
 386                 obtainDetailedTaxonomicInformation();
 387             }
 388             else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
 389                 if ( isSubtreeDisplayed() ) {
 390                     return;
 391                 }
 392                 obtainDetailedTaxonomicInformationDelete();
 393             }
 394             else if ( o == _obtain_seq_information_jmi ) {
 395                 obtainSequenceInformation();
 396             }
 397             else if ( o == _read_values_jmi ) {
 398                 if ( isSubtreeDisplayed() ) {
 399                     return;
 400                 }
 401                 addExpressionValuesFromFile();
 402             }
 403             else if ( o == _read_seqs_jmi ) {
 404                 if ( isSubtreeDisplayed() ) {
 405                     return;
 406                 }
 407                 addSequencesFromFile();
 408             }
 409             else if ( o == _move_node_names_to_tax_sn_jmi ) {
 410                 moveNodeNamesToTaxSn();
 411             }
 412             else if ( o == _move_node_names_to_seq_names_jmi ) {
 413                 moveNodeNamesToSeqNames();
 414             }
 415             else if ( o == _extract_tax_code_from_node_names_jmi ) {
 416                 extractTaxDataFromNodeNames();
 417             }
 418             else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {
 419                 updateOptions( getOptions() );
 420             }
 421             else if ( o == _replace_underscores_cbmi ) {
 422                 if ( ( _extract_taxonomy_no_rbmi != null ) && !_extract_taxonomy_no_rbmi.isSelected() ) {
 423                     _extract_taxonomy_no_rbmi.setSelected( true );
 424                 }
 425                 updateOptions( getOptions() );
 426             }
 427             else if ( o == _allow_errors_in_distance_to_parent_cbmi ) {
 428                 updateOptions( getOptions() );
 429             }
 430             else if ( o == _collapse_below_threshold ) {
 431                 if ( isSubtreeDisplayed() ) {
 432                     return;
 433                 }
 434                 collapseBelowThreshold();
 435             }
 436
 437             else if ( o == _collapse_below_branch_length ) {
 438                 if ( isSubtreeDisplayed() ) {
 439                     return;
 440                 }
 441                 collapseBelowBranchLengthThreshold();
 442             }
 443             else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
 444                     || ( o == _extract_taxonomy_agressive_rbmi ) ) {
 445                 if ( _replace_underscores_cbmi != null ) {
 446                     _replace_underscores_cbmi.setSelected( false );
 447                 }
 448                 updateOptions( getOptions() );
 449             }
 450             else if ( o == _extract_taxonomy_no_rbmi ) {
 451                 updateOptions( getOptions() );
 452             }
 453             else if ( o == _inference_from_msa_item ) {
 454                 executePhyleneticInference( false );
 455             }
 456             else if ( o == _inference_from_seqs_item ) {
 457                 executePhyleneticInference( true );
 458             }
 459             _contentpane.repaint();
 460         }
 461         catch ( final Exception ex ) {
 462             AptxUtil.unexpectedException( ex );
 463         }
 464         catch ( final Error err ) {
 465             AptxUtil.unexpectedError( err );
 466         }
 467     }
 468
 469     public void end() {
 470         _mainpanel.terminate();
 471         _contentpane.removeAll();
 472         setVisible( false );
 473         dispose();
 474     }
 475
 476     @Override
 477     public MainPanel getMainPanel() {
 478         return _mainpanel;
 479     }
 480
 481     public Msa getMsa() {
 482         return _msa;
 483     }
 484
 485     public File getMsaFile() {
 486         return _msa_file;
 487     }
 488
 489     public List<MolecularSequence> getSeqs() {
 490         return _seqs;
 491     }
 492
 493     public File getSeqsFile() {
 494         return _seqs_file;
 495     }
 496
 497     public void readMsaFromFile() {
 498         // Set an initial directory if none set yet
 499         final File my_dir = getCurrentDir();
 500         _msa_filechooser.setMultiSelectionEnabled( false );
 501         // Open file-open dialog and set current directory
 502         if ( my_dir != null ) {
 503             _msa_filechooser.setCurrentDirectory( my_dir );
 504         }
 505         final int result = _msa_filechooser.showOpenDialog( _contentpane );
 506         // All done: get the msa
 507         final File file = _msa_filechooser.getSelectedFile();
 508         setCurrentDir( _msa_filechooser.getCurrentDirectory() );
 509         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 510             setMsaFile( null );
 511             setMsa( null );
 512             Msa msa = null;
 513             try {
 514                 final InputStream is = new FileInputStream( file );
 515                 if ( FastaParser.isLikelyFasta( file ) ) {
 516                     msa = FastaParser.parseMsa( is );
 517                 }
 518                 else {
 519                     msa = GeneralMsaParser.parse( is );
 520                 }
 521             }
 522             catch ( final MsaFormatException e ) {
 523                 setArrowCursor();
 524                 JOptionPane.showMessageDialog( this,
 525                                                e.getLocalizedMessage(),
 526                                                "Multiple sequence alignment format error",
 527                                                JOptionPane.ERROR_MESSAGE );
 528                 return;
 529             }
 530             catch ( final IOException e ) {
 531                 setArrowCursor();
 532                 JOptionPane.showMessageDialog( this,
 533                                                e.getLocalizedMessage(),
 534                                                "Failed to read multiple sequence alignment",
 535                                                JOptionPane.ERROR_MESSAGE );
 536                 return;
 537             }
 538             catch ( final IllegalArgumentException e ) {
 539                 setArrowCursor();
 540                 JOptionPane.showMessageDialog( this,
 541                                                e.getLocalizedMessage(),
 542                                                "Unexpected error during reading of multiple sequence alignment",
 543                                                JOptionPane.ERROR_MESSAGE );
 544                 return;
 545             }
 546             catch ( final Exception e ) {
 547                 setArrowCursor();
 548                 e.printStackTrace();
 549                 JOptionPane.showMessageDialog( this,
 550                                                e.getLocalizedMessage(),
 551                                                "Unexpected error during reading of multiple sequence alignment",
 552                                                JOptionPane.ERROR_MESSAGE );
 553                 return;
 554             }
 555             if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
 556                 JOptionPane.showMessageDialog( this,
 557                                                "Multiple sequence alignment is empty",
 558                                                "Illegal Multiple Sequence Alignment",
 559                                                JOptionPane.ERROR_MESSAGE );
 560                 return;
 561             }
 562             if ( msa.getNumberOfSequences() < 4 ) {
 563                 JOptionPane.showMessageDialog( this,
 564                                                "Multiple sequence alignment needs to contain at least 3 sequences",
 565                                                "Illegal multiple sequence alignment",
 566                                                JOptionPane.ERROR_MESSAGE );
 567                 return;
 568             }
 569             if ( msa.getLength() < 2 ) {
 570                 JOptionPane.showMessageDialog( this,
 571                                                "Multiple sequence alignment needs to contain at least 2 residues",
 572                                                "Illegal multiple sequence alignment",
 573                                                JOptionPane.ERROR_MESSAGE );
 574                 return;
 575             }
 576             System.gc();
 577             setMsaFile( _msa_filechooser.getSelectedFile() );
 578             setMsa( msa );
 579         }
 580     }
 581
 582     public void readSeqsFromFileforPI() {
 583         // Set an initial directory if none set yet
 584         final File my_dir = getCurrentDir();
 585         _seqs_pi_filechooser.setMultiSelectionEnabled( false );
 586         // Open file-open dialog and set current directory
 587         if ( my_dir != null ) {
 588             _seqs_pi_filechooser.setCurrentDirectory( my_dir );
 589         }
 590         final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );
 591         // All done: get the seqs
 592         final File file = _seqs_pi_filechooser.getSelectedFile();
 593         setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );
 594         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 595             setSeqsFile( null );
 596             setSeqs( null );
 597             List<MolecularSequence> seqs = null;
 598             try {
 599                 if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
 600                     seqs = FastaParser.parse( new FileInputStream( file ) );
 601                     for( final MolecularSequence seq : seqs ) {
 602                         System.out.println( SequenceWriter.toFasta( seq, 60 ) );
 603                     }
 604                 }
 605                 else {
 606                     //TODO error
 607                 }
 608             }
 609             catch ( final MsaFormatException e ) {
 610                 setArrowCursor();
 611                 JOptionPane.showMessageDialog( this,
 612                                                e.getLocalizedMessage(),
 613                                                "Multiple sequence file format error",
 614                                                JOptionPane.ERROR_MESSAGE );
 615                 return;
 616             }
 617             catch ( final IOException e ) {
 618                 setArrowCursor();
 619                 JOptionPane.showMessageDialog( this,
 620                                                e.getLocalizedMessage(),
 621                                                "Failed to read multiple sequence file",
 622                                                JOptionPane.ERROR_MESSAGE );
 623                 return;
 624             }
 625             catch ( final IllegalArgumentException e ) {
 626                 setArrowCursor();
 627                 JOptionPane.showMessageDialog( this,
 628                                                e.getLocalizedMessage(),
 629                                                "Unexpected error during reading of multiple sequence file",
 630                                                JOptionPane.ERROR_MESSAGE );
 631                 return;
 632             }
 633             catch ( final Exception e ) {
 634                 setArrowCursor();
 635                 e.printStackTrace();
 636                 JOptionPane.showMessageDialog( this,
 637                                                e.getLocalizedMessage(),
 638                                                "Unexpected error during reading of multiple sequence file",
 639                                                JOptionPane.ERROR_MESSAGE );
 640                 return;
 641             }
 642             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 643                 JOptionPane.showMessageDialog( this,
 644                                                "Multiple sequence file is empty",
 645                                                "Illegal multiple sequence file",
 646                                                JOptionPane.ERROR_MESSAGE );
 647                 return;
 648             }
 649             if ( seqs.size() < 4 ) {
 650                 JOptionPane.showMessageDialog( this,
 651                                                "Multiple sequence file needs to contain at least 3 sequences",
 652                                                "Illegal multiple sequence file",
 653                                                JOptionPane.ERROR_MESSAGE );
 654                 return;
 655             }
 656             //  if ( msa.getLength() < 2 ) {
 657             //       JOptionPane.showMessageDialog( this,
 658             //                                      "Multiple sequence alignment needs to contain at least 2 residues",
 659             //                                      "Illegal multiple sequence file",
 660             //                                      JOptionPane.ERROR_MESSAGE );
 661             //       return;
 662             //   }
 663             System.gc();
 664             setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
 665             setSeqs( seqs );
 666         }
 667     }
 668
 669     private void addExpressionValuesFromFile() {
 670         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
 671             JOptionPane.showMessageDialog( this,
 672                                            "Need to load evolutionary tree first",
 673                                            "Can Not Read Expression Values",
 674                                            JOptionPane.WARNING_MESSAGE );
 675             return;
 676         }
 677         final File my_dir = getCurrentDir();
 678         if ( my_dir != null ) {
 679             _values_filechooser.setCurrentDirectory( my_dir );
 680         }
 681         final int result = _values_filechooser.showOpenDialog( _contentpane );
 682         final File file = _values_filechooser.getSelectedFile();
 683         if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
 684             BasicTable<String> t = null;
 685             try {
 686                 t = BasicTableParser.parse( file, '\t' );
 687                 if ( t.getNumberOfColumns() < 2 ) {
 688                     t = BasicTableParser.parse( file, ',' );
 689                 }
 690                 if ( t.getNumberOfColumns() < 2 ) {
 691                     t = BasicTableParser.parse( file, ' ' );
 692                 }
 693             }
 694             catch ( final IOException e ) {
 695                 JOptionPane.showMessageDialog( this,
 696                                                e.getMessage(),
 697                                                "Could Not Read Expression Value Table",
 698                                                JOptionPane.ERROR_MESSAGE );
 699                 return;
 700             }
 701             if ( t.getNumberOfColumns() < 2 ) {
 702                 JOptionPane.showMessageDialog( this,
 703                                                "Table contains " + t.getNumberOfColumns() + " column(s)",
 704                                                "Problem with Expression Value Table",
 705                                                JOptionPane.ERROR_MESSAGE );
 706                 return;
 707             }
 708             if ( t.getNumberOfRows() < 1 ) {
 709                 JOptionPane.showMessageDialog( this,
 710                                                "Table contains zero rows",
 711                                                "Problem with Expression Value Table",
 712                                                JOptionPane.ERROR_MESSAGE );
 713                 return;
 714             }
 715             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
 716             if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
 717                 JOptionPane.showMessageDialog( this,
 718                                                "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
 719                                                        + phy.getNumberOfExternalNodes() + " external nodes",
 720                                                "Warning",
 721                                                JOptionPane.WARNING_MESSAGE );
 722             }
 723             final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 724             int not_found = 0;
 725             for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
 726                 final PhylogenyNode node = iter.next();
 727                 final String node_name = node.getName();
 728                 if ( !ForesterUtil.isEmpty( node_name ) ) {
 729                     int row = -1;
 730                     try {
 731                         row = t.findRow( node_name );
 732                     }
 733                     catch ( final IllegalArgumentException e ) {
 734                         JOptionPane.showMessageDialog( this,
 735                                                        e.getMessage(),
 736                                                        "Error Mapping Node Identifiers to Expression Value Identifiers",
 737                                                        JOptionPane.ERROR_MESSAGE );
 738                         return;
 739                     }
 740                     if ( row < 0 ) {
 741                         if ( node.isExternal() ) {
 742                             not_found++;
 743                         }
 744                         continue;
 745                     }
 746                     final List<Double> l = new ArrayList<Double>();
 747                     for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
 748                         double d = -100;
 749                         try {
 750                             d = Double.parseDouble( t.getValueAsString( col, row ) );
 751                         }
 752                         catch ( final NumberFormatException e ) {
 753                             JOptionPane.showMessageDialog( this,
 754                                                            "Could not parse \"" + t.getValueAsString( col, row )
 755                                                                    + "\" into a decimal value",
 756                                                            "Issue with Expression Value Table",
 757                                                            JOptionPane.ERROR_MESSAGE );
 758                             return;
 759                         }
 760                         stats.addValue( d );
 761                         l.add( d );
 762                     }
 763                     if ( !l.isEmpty() ) {
 764
 765                         node.getNodeData().setVector( l );
 766                     }
 767                 }
 768             }
 769             if ( not_found > 0 ) {
 770                 JOptionPane
 771                         .showMessageDialog( this,
 772                                             "Could not fine expression values for " + not_found + " external node(s)",
 773                                             "Warning",
 774                                             JOptionPane.WARNING_MESSAGE );
 775             }
 776             getCurrentTreePanel().setStatisticsForExpressionValues( stats );
 777         }
 778     }
 779
 780     private void addSequencesFromFile() {
 781         if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
 782             JOptionPane.showMessageDialog( this,
 783                                            "Need to load evolutionary tree first",
 784                                            "Can Not Read Sequences",
 785                                            JOptionPane.WARNING_MESSAGE );
 786             return;
 787         }
 788         final File my_dir = getCurrentDir();
 789         if ( my_dir != null ) {
 790             _sequences_filechooser.setCurrentDirectory( my_dir );
 791         }
 792         final int result = _sequences_filechooser.showOpenDialog( _contentpane );
 793         final File file = _sequences_filechooser.getSelectedFile();
 794         List<MolecularSequence> seqs = null;
 795         if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {
 796             try {
 797                 final FileInputStream fis1 = new FileInputStream( file );
 798                 if ( FastaParser.isLikelyFasta( fis1 ) ) {
 799                     final FileInputStream fis2 = new FileInputStream( file );
 800                     seqs = FastaParser.parse( fis2 );
 801                     try {
 802                         fis2.close();
 803                     }
 804                     catch ( final Exception e ) {
 805                         // Ignore.
 806                     }
 807                 }
 808                 else {
 809                     JOptionPane.showMessageDialog( this,
 810                                                    "Format does not appear to be Fasta",
 811                                                    "Multiple sequence file format error",
 812                                                    JOptionPane.ERROR_MESSAGE );
 813                     return;
 814                 }
 815                 try {
 816                     fis1.close();
 817                 }
 818                 catch ( final Exception e ) {
 819                     // Ignore.
 820                 }
 821             }
 822             catch ( final MsaFormatException e ) {
 823                 setArrowCursor();
 824                 JOptionPane.showMessageDialog( this,
 825                                                e.getLocalizedMessage(),
 826                                                "Multiple sequence file format error",
 827                                                JOptionPane.ERROR_MESSAGE );
 828                 return;
 829             }
 830             catch ( final IOException e ) {
 831                 setArrowCursor();
 832                 JOptionPane.showMessageDialog( this,
 833                                                e.getLocalizedMessage(),
 834                                                "Failed to read multiple sequence file",
 835                                                JOptionPane.ERROR_MESSAGE );
 836                 return;
 837             }
 838             catch ( final Exception e ) {
 839                 setArrowCursor();
 840                 e.printStackTrace();
 841                 JOptionPane.showMessageDialog( this,
 842                                                e.getLocalizedMessage(),
 843                                                "Unexpected error during reading of multiple sequence file",
 844                                                JOptionPane.ERROR_MESSAGE );
 845                 return;
 846             }
 847             if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
 848                 JOptionPane.showMessageDialog( this,
 849                                                "Multiple sequence file is empty",
 850                                                "Empty multiple sequence file",
 851                                                JOptionPane.ERROR_MESSAGE );
 852                 setArrowCursor();
 853                 return;
 854             }
 855         }
 856         if ( seqs != null ) {
 857             for( final MolecularSequence seq : seqs ) {
 858                 System.out.println( seq.getIdentifier() );
 859             }
 860             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
 861             int total_counter = 0;
 862             int attached_counter = 0;
 863             for( final MolecularSequence seq : seqs ) {
 864                 ++total_counter;
 865                 final String seq_name = seq.getIdentifier();
 866                 if ( !ForesterUtil.isEmpty( seq_name ) ) {
 867                     List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );
 868                     if ( nodes.isEmpty() ) {
 869                         nodes = phy.getNodesViaSequenceSymbol( seq_name );
 870                     }
 871                     if ( nodes.isEmpty() ) {
 872                         nodes = phy.getNodesViaGeneName( seq_name );
 873                     }
 874                     if ( nodes.isEmpty() ) {
 875                         nodes = phy.getNodes( seq_name );
 876                     }
 877                     if ( nodes.size() > 1 ) {
 878                         JOptionPane.showMessageDialog( this,
 879                                                        "Sequence name \"" + seq_name + "\" is not unique",
 880                                                        "Sequence name not unique",
 881                                                        JOptionPane.ERROR_MESSAGE );
 882                         setArrowCursor();
 883                         return;
 884                     }
 885                     final String[] a = seq_name.split( "\\s" );
 886                     if ( nodes.isEmpty() && ( a.length > 1 ) ) {
 887                         final String seq_name_split = a[ 0 ];
 888                         nodes = phy.getNodesViaSequenceName( seq_name_split );
 889                         if ( nodes.isEmpty() ) {
 890                             nodes = phy.getNodesViaSequenceSymbol( seq_name_split );
 891                         }
 892                         if ( nodes.isEmpty() ) {
 893                             nodes = phy.getNodes( seq_name_split );
 894                         }
 895                         if ( nodes.size() > 1 ) {
 896                             JOptionPane.showMessageDialog( this,
 897                                                            "Split sequence name \"" + seq_name_split
 898                                                                    + "\" is not unique",
 899                                                            "Sequence name not unique",
 900                                                            JOptionPane.ERROR_MESSAGE );
 901                             setArrowCursor();
 902                             return;
 903                         }
 904                     }
 905                     if ( nodes.size() == 1 ) {
 906                         ++attached_counter;
 907                         final PhylogenyNode n = nodes.get( 0 );
 908                         if ( !n.getNodeData().isHasSequence() ) {
 909                             n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
 910                         }
 911                         n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
 912                         if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
 913                             n.getNodeData().getSequence().setName( seq_name );
 914                         }
 915                     }
 916                 }
 917             }
 918             if ( attached_counter > 0 ) {
 919                 int ext_nodes = 0;
 920                 int ext_nodes_with_seq = 0;
 921                 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 922                     ++ext_nodes;
 923                     final PhylogenyNode n = iter.next();
 924                     if ( n.getNodeData().isHasSequence()
 925                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
 926                         ++ext_nodes_with_seq;
 927                     }
 928                 }
 929                 final String s;
 930                 if ( ext_nodes == ext_nodes_with_seq ) {
 931                     s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";
 932                 }
 933                 else {
 934                     s = ext_nodes_with_seq + " out of " + ext_nodes
 935                             + " external nodes now have a molecular sequence attached to them.";
 936                 }
 937                 if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
 938                     JOptionPane.showMessageDialog( this,
 939                                                    "Attached all " + total_counter + " sequences to tree nodes.\n" + s,
 940                                                    "All sequences attached",
 941                                                    JOptionPane.INFORMATION_MESSAGE );
 942                 }
 943                 else {
 944                     JOptionPane.showMessageDialog( this,
 945                                                    "Attached " + attached_counter + " sequences out of a total of "
 946                                                            + total_counter + " sequences.\n" + s,
 947                                                    attached_counter + " sequences attached",
 948                                                    JOptionPane.WARNING_MESSAGE );
 949                 }
 950             }
 951             else {
 952                 JOptionPane.showMessageDialog( this,
 953                                                "No maching tree node for any of the " + total_counter + " sequences",
 954                                                "Could not attach any sequences",
 955                                                JOptionPane.ERROR_MESSAGE );
 956             }
 957         }
 958     }
 959
 960     private void closeCurrentPane() {
 961         if ( getMainPanel().getCurrentTreePanel() != null ) {
 962             if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
 963                 final int r = JOptionPane.showConfirmDialog( this,
 964                                                              "Close tab despite potentially unsaved changes?",
 965                                                              "Close Tab?",
 966                                                              JOptionPane.YES_NO_OPTION );
 967                 if ( r != JOptionPane.YES_OPTION ) {
 968                     return;
 969                 }
 970             }
 971             getMainPanel().closeCurrentPane();
 972             activateSaveAllIfNeeded();
 973         }
 974     }
 975
 976     private void collapseBelowThreshold( final Phylogeny phy ) {
 977         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 978         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
 979         double min_support = Double.MAX_VALUE;
 980         boolean conf_present = false;
 981         while ( it.hasNext() ) {
 982             final PhylogenyNode n = it.next();
 983             if ( !n.isExternal() && !n.isRoot() ) {
 984                 final List<Confidence> c = n.getBranchData().getConfidences();
 985                 if ( ( c != null ) && ( c.size() > 0 ) ) {
 986                     conf_present = true;
 987                     double max = 0;
 988                     for( final Confidence confidence : c ) {
 989                         if ( confidence.getValue() > max ) {
 990                             max = confidence.getValue();
 991                         }
 992                     }
 993                     if ( max < getMinNotCollapseConfidenceValue() ) {
 994                         to_be_removed.add( n );
 995                     }
 996                     if ( max < min_support ) {
 997                         min_support = max;
 998                     }
 999                 }
1000             }
1001         }
1002         if ( conf_present ) {
1003             for( final PhylogenyNode node : to_be_removed ) {
1004                 PhylogenyMethods.removeNode( node, phy );
1005             }
1006             if ( to_be_removed.size() > 0 ) {
1007                 phy.externalNodesHaveChanged();
1008                 phy.clearHashIdToNodeMap();
1009                 phy.recalculateNumberOfExternalDescendants( true );
1010                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1011                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1012                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1013                 getCurrentTreePanel().setNodeInPreorderToNull();
1014                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1015                 getCurrentTreePanel().resetPreferredSize();
1016                 getCurrentTreePanel().setEdited( true );
1017                 getCurrentTreePanel().repaint();
1018                 repaint();
1019             }
1020             if ( to_be_removed.size() > 0 ) {
1021                 JOptionPane.showMessageDialog( this,
1022                                                "Collapsed " + to_be_removed.size()
1023                                                        + " branches with\nconfidence values below "
1024                                                        + getMinNotCollapseConfidenceValue(),
1025                                                "Collapsed " + to_be_removed.size() + " branches",
1026                                                JOptionPane.INFORMATION_MESSAGE );
1027             }
1028             else {
1029                 JOptionPane.showMessageDialog( this,
1030                                                "No branch collapsed,\nminimum confidence value per branch is "
1031                                                        + min_support,
1032                                                "No branch collapsed",
1033                                                JOptionPane.INFORMATION_MESSAGE );
1034             }
1035         }
1036         else {
1037             JOptionPane.showMessageDialog( this,
1038                                            "No branch collapsed because no confidence values present",
1039                                            "No confidence values present",
1040                                            JOptionPane.INFORMATION_MESSAGE );
1041         }
1042     }
1043
1044     private void collapseBelowBranchLengthThreshold() {
1045         if ( getCurrentTreePanel() != null ) {
1046             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1047             if ( ( phy != null ) && !phy.isEmpty() ) {
1048                 final String s = ( String ) JOptionPane.showInputDialog( this,
1049                                                                          "Please enter the minimum branch length value\n",
1050                                                                          "Minimal Branch Length Value",
1051                                                                          JOptionPane.QUESTION_MESSAGE,
1052                                                                          null,
1053                                                                          null,
1054                                                                          getMinNotCollapseBlValue() );
1055                 if ( !ForesterUtil.isEmpty( s ) ) {
1056                     boolean success = true;
1057                     double m = 0.0;
1058                     final String m_str = s.trim();
1059                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1060                         try {
1061                             m = Double.parseDouble( m_str );
1062                         }
1063                         catch ( final Exception ex ) {
1064                             success = false;
1065                         }
1066                     }
1067                     else {
1068                         success = false;
1069                     }
1070                     if ( success && ( m >= 0.0 ) ) {
1071                         setMinNotCollapseBlValue( m );
1072                         collapseBl( phy );
1073                     }
1074                 }
1075             }
1076         }
1077     }
1078
1079     private void collapseBelowThreshold() {
1080         if ( getCurrentTreePanel() != null ) {
1081             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1082             if ( ( phy != null ) && !phy.isEmpty() ) {
1083                 final String s = ( String ) JOptionPane.showInputDialog( this,
1084                                                                          "Please enter the minimum confidence value\n",
1085                                                                          "Minimal Confidence Value",
1086                                                                          JOptionPane.QUESTION_MESSAGE,
1087                                                                          null,
1088                                                                          null,
1089                                                                          getMinNotCollapseConfidenceValue() );
1090                 if ( !ForesterUtil.isEmpty( s ) ) {
1091                     boolean success = true;
1092                     double m = 0.0;
1093                     final String m_str = s.trim();
1094                     if ( !ForesterUtil.isEmpty( m_str ) ) {
1095                         try {
1096                             m = Double.parseDouble( m_str );
1097                         }
1098                         catch ( final Exception ex ) {
1099                             success = false;
1100                         }
1101                     }
1102                     else {
1103                         success = false;
1104                     }
1105                     if ( success && ( m >= 0.0 ) ) {
1106                         setMinNotCollapseConfidenceValue( m );
1107                         collapseBelowThreshold( phy );
1108                     }
1109                 }
1110             }
1111         }
1112     }
1113
1114     private void collapseBl( final Phylogeny phy ) {
1115         final PhylogenyNodeIterator it = phy.iteratorPostorder();
1116         final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
1117         double min_bl = Double.MAX_VALUE;
1118         boolean bl_present = false;
1119         while ( it.hasNext() ) {
1120             final PhylogenyNode n = it.next();
1121             if ( !n.isExternal() && !n.isRoot() ) {
1122                 final double bl = n.getDistanceToParent();
1123                 if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
1124                     bl_present = true;
1125                     if ( bl < getMinNotCollapseBlValue() ) {
1126                         to_be_removed.add( n );
1127                     }
1128                     if ( bl < min_bl ) {
1129                         min_bl = bl;
1130                     }
1131                 }
1132             }
1133         }
1134         if ( bl_present ) {
1135             for( final PhylogenyNode node : to_be_removed ) {
1136                 PhylogenyMethods.removeNode( node, phy );
1137             }
1138             if ( to_be_removed.size() > 0 ) {
1139                 phy.externalNodesHaveChanged();
1140                 phy.clearHashIdToNodeMap();
1141                 phy.recalculateNumberOfExternalDescendants( true );
1142                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
1143                 getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
1144                 getCurrentTreePanel().calculateLongestExtNodeInfo();
1145                 getCurrentTreePanel().setNodeInPreorderToNull();
1146                 getCurrentTreePanel().recalculateMaxDistanceToRoot();
1147                 getCurrentTreePanel().resetPreferredSize();
1148                 getCurrentTreePanel().setEdited( true );
1149                 getCurrentTreePanel().repaint();
1150                 repaint();
1151             }
1152             if ( to_be_removed.size() > 0 ) {
1153                 JOptionPane.showMessageDialog( this,
1154                                                "Collapsed " + to_be_removed.size()
1155                                                        + " branches with\nbranch length values below "
1156                                                        + getMinNotCollapseBlValue(),
1157                                                "Collapsed " + to_be_removed.size() + " branches",
1158                                                JOptionPane.INFORMATION_MESSAGE );
1159             }
1160             else {
1161                 JOptionPane.showMessageDialog( this,
1162                                                "No branch collapsed,\nminimum branch length is " + min_bl,
1163                                                "No branch collapsed",
1164                                                JOptionPane.INFORMATION_MESSAGE );
1165             }
1166         }
1167         else {
1168             JOptionPane.showMessageDialog( this,
1169                                            "No branch collapsed because no branch length values present",
1170                                            "No branch length values present",
1171                                            JOptionPane.INFORMATION_MESSAGE );
1172         }
1173     }
1174
1175     private PhyloXmlParser createPhyloXmlParser() {
1176         PhyloXmlParser xml_parser = null;
1177         if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {
1178             try {
1179                 xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
1180             }
1181             catch ( final Exception e ) {
1182                 JOptionPane.showMessageDialog( this,
1183                                                e.getLocalizedMessage(),
1184                                                "failed to create validating XML parser",
1185                                                JOptionPane.WARNING_MESSAGE );
1186             }
1187         }
1188         if ( xml_parser == null ) {
1189             xml_parser = PhyloXmlParser.createPhyloXmlParser();
1190         }
1191         return xml_parser;
1192     }
1193
1194     private void executePhyleneticInference( final boolean from_unaligned_seqs ) {
1195         final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,
1196                                                                       getPhylogeneticInferenceOptions(),
1197                                                                       from_unaligned_seqs );
1198         dialog.activate();
1199         if ( dialog.getValue() == JOptionPane.OK_OPTION ) {
1200             if ( !from_unaligned_seqs ) {
1201                 if ( getMsa() != null ) {
1202                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
1203                                                                                     getPhylogeneticInferenceOptions()
1204                                                                                             .copy(),
1205                                                                                     this );
1206                     new Thread( inferrer ).start();
1207                 }
1208                 else {
1209                     JOptionPane.showMessageDialog( this,
1210                                                    "No multiple sequence alignment selected",
1211                                                    "Phylogenetic Inference Not Launched",
1212                                                    JOptionPane.WARNING_MESSAGE );
1213                 }
1214             }
1215             else {
1216                 if ( getSeqs() != null ) {
1217                     final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
1218                                                                                     getPhylogeneticInferenceOptions()
1219                                                                                             .copy(),
1220                                                                                     this );
1221                     new Thread( inferrer ).start();
1222                 }
1223                 else {
1224                     JOptionPane.showMessageDialog( this,
1225                                                    "No input sequences selected",
1226                                                    "Phylogenetic Inference Not Launched",
1227                                                    JOptionPane.WARNING_MESSAGE );
1228                 }
1229             }
1230         }
1231     }
1232
1233     private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {
1234         final StringBuilder sb = new StringBuilder();
1235         final StringBuilder sb_failed = new StringBuilder();
1236         int counter = 0;
1237         int counter_failed = 0;
1238         if ( getCurrentTreePanel() != null ) {
1239             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1240             if ( ( phy != null ) && !phy.isEmpty() ) {
1241                 final PhylogenyNodeIterator it = phy.iteratorExternalForward();
1242                 while ( it.hasNext() ) {
1243                     final PhylogenyNode n = it.next();
1244                     final String name = n.getName().trim();
1245                     if ( !ForesterUtil.isEmpty( name ) ) {
1246                         final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
1247                                                                                        TAXONOMY_EXTRACTION.AGGRESSIVE );
1248                         if ( !ForesterUtil.isEmpty( nt ) ) {
1249                             if ( counter < 15 ) {
1250                                 sb.append( name + ": " + nt + "\n" );
1251                             }
1252                             else if ( counter == 15 ) {
1253                                 sb.append( "...\n" );
1254                             }
1255                             counter++;
1256                         }
1257                         else {
1258                             if ( counter_failed < 15 ) {
1259                                 sb_failed.append( name + "\n" );
1260                             }
1261                             else if ( counter_failed == 15 ) {
1262                                 sb_failed.append( "...\n" );
1263                             }
1264                             counter_failed++;
1265                         }
1266                     }
1267                 }
1268                 if ( counter > 0 ) {
1269                     String failed = "";
1270                     String all = "all ";
1271                     if ( counter_failed > 0 ) {
1272                         all = "";
1273                         failed = "\nCould not extract taxonomic data for " + counter_failed + " named external nodes:\n"
1274                                 + sb_failed;
1275                     }
1276                     JOptionPane.showMessageDialog( this,
1277                                                    "Extracted taxonomic data from " + all + counter
1278                                                            + " named external nodes:\n" + sb.toString() + failed,
1279                                                    "Taxonomic Data Extraction Completed",
1280                                                    counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
1281                                                            : JOptionPane.INFORMATION_MESSAGE );
1282                 }
1283                 else {
1284                     JOptionPane.showMessageDialog( this,
1285                                                    "Could not extract any taxonomic data.\nMaybe node names are empty\n"
1286                                                            + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
1287                                                            + "or nodes already have taxonomic data?\n",
1288                                                    "No Taxonomic Data Extracted",
1289                                                    JOptionPane.ERROR_MESSAGE );
1290                 }
1291             }
1292         }
1293     }
1294
1295     private double getMinNotCollapseBlValue() {
1296         return _min_not_collapse_bl;
1297     }
1298
1299     private double getMinNotCollapseConfidenceValue() {
1300         return _min_not_collapse;
1301     }
1302
1303     private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {
1304         if ( _phylogenetic_inference_options == null ) {
1305             _phylogenetic_inference_options = new PhylogeneticInferenceOptions();
1306         }
1307         return _phylogenetic_inference_options;
1308     }
1309
1310     private boolean isUnsavedDataPresent() {
1311         final List<TreePanel> tps = getMainPanel().getTreePanels();
1312         for( final TreePanel tp : tps ) {
1313             if ( tp.isEdited() ) {
1314                 return true;
1315             }
1316         }
1317         return false;
1318     }
1319
1320     private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
1321         if ( getCurrentTreePanel() != null ) {
1322             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1323             if ( ( phy != null ) && !phy.isEmpty() ) {
1324                 PhylogenyMethods.transferNodeNameToField( phy,
1325                                                           PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME,
1326                                                           false );
1327             }
1328         }
1329     }
1330
1331     private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
1332         if ( getCurrentTreePanel() != null ) {
1333             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1334             if ( ( phy != null ) && !phy.isEmpty() ) {
1335                 PhylogenyMethods.transferNodeNameToField( phy,
1336                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
1337                                                           false );
1338             }
1339         }
1340     }
1341
1342     private void newTree() {
1343         final Phylogeny[] phys = new Phylogeny[ 1 ];
1344         final Phylogeny phy = new Phylogeny();
1345         final PhylogenyNode node = new PhylogenyNode();
1346         phy.setRoot( node );
1347         phy.setRooted( true );
1348         phys[ 0 ] = phy;
1349         AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
1350         _mainpanel.getControlPanel().showWhole();
1351         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1352         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1353
1354         getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
1355
1356         activateSaveAllIfNeeded();
1357         System.gc();
1358     }
1359
1360     private void obtainDetailedTaxonomicInformation() {
1361         if ( getCurrentTreePanel() != null ) {
1362             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1363             if ( ( phy != null ) && !phy.isEmpty() ) {
1364                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1365                                                                        _mainpanel.getCurrentTreePanel(),
1366                                                                        phy.copy(),
1367                                                                        false,
1368                                                                        true );
1369                 new Thread( t ).start();
1370             }
1371         }
1372     }
1373
1374     private void obtainDetailedTaxonomicInformationDelete() {
1375         if ( getCurrentTreePanel() != null ) {
1376             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1377             if ( ( phy != null ) && !phy.isEmpty() ) {
1378                 final TaxonomyDataManager t = new TaxonomyDataManager( this,
1379                                                                        _mainpanel.getCurrentTreePanel(),
1380                                                                        phy.copy(),
1381                                                                        true,
1382                                                                        true );
1383                 new Thread( t ).start();
1384             }
1385         }
1386     }
1387
1388     private void obtainSequenceInformation() {
1389         if ( getCurrentTreePanel() != null ) {
1390             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
1391             if ( ( phy != null ) && !phy.isEmpty() ) {
1392                 final SequenceDataRetriver u = new SequenceDataRetriver( this,
1393                                                                          _mainpanel.getCurrentTreePanel(),
1394                                                                          phy.copy() );
1395                 new Thread( u ).start();
1396             }
1397         }
1398     }
1399
1400     private void preProcessTreesUponReading( final Phylogeny[] phys ) {
1401         for( final Phylogeny phy : phys ) {
1402             if ( ( phy != null ) && !phy.isEmpty() ) {
1403                 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
1404                     final PhylogenyNode n = it.next();
1405                     if ( n.isExternal() ) {
1406                         if ( n.getNodeData().isHasSequence() ) {
1407                             final Sequence s = n.getNodeData().getSequence();
1408                             if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {
1409                                 if ( ( s.getAccession() != null )
1410                                         && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
1411                                     s.setGeneName( s.getAccession().getValue() );
1412                                 }
1413                                 else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
1414                                     s.setGeneName( n.getName() );
1415                                 }
1416                             }
1417                         }
1418                     }
1419                 }
1420             }
1421         }
1422     }
1423
1424     private void readPhylogeniesFromFile() {
1425         boolean exception = false;
1426         Phylogeny[] phys = null;
1427         // Set an initial directory if none set yet
1428         final File my_dir = getCurrentDir();
1429         // Open file-open dialog and set current directory
1430         if ( my_dir != null ) {
1431             _open_filechooser.setCurrentDirectory( my_dir );
1432         }
1433         final int result = _open_filechooser.showOpenDialog( _contentpane );
1434         // All done: get the file
1435         final File[] files = _open_filechooser.getSelectedFiles();
1436         setCurrentDir( _open_filechooser.getCurrentDirectory() );
1437         boolean nhx_or_nexus = false;
1438         if ( ( files != null ) && ( files.length > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1439             for( final File file : files ) {
1440                 if ( ( file != null ) && !file.isDirectory() ) {
1441                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1442                         _mainpanel.getCurrentTreePanel().setWaitCursor();
1443                     }
1444                     else {
1445                         _mainpanel.setWaitCursor();
1446                     }
1447                     if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )
1448                             || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {
1449                         try {
1450                             final NHXParser nhx = new NHXParser();
1451                             setSpecialOptionsForNhxParser( nhx );
1452                             phys = PhylogenyMethods.readPhylogenies( nhx, file );
1453                             nhx_or_nexus = true;
1454                         }
1455                         catch ( final Exception e ) {
1456                             exception = true;
1457                             exceptionOccuredDuringOpenFile( e );
1458                         }
1459                     }
1460                     else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {
1461                         warnIfNotPhyloXmlValidation( getConfiguration() );
1462                         try {
1463                             final PhyloXmlParser xml_parser = createPhyloXmlParser();
1464                             phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
1465                         }
1466                         catch ( final Exception e ) {
1467                             exception = true;
1468                             exceptionOccuredDuringOpenFile( e );
1469                         }
1470                     }
1471                     else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {
1472                         try {
1473                             phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1474                         }
1475                         catch ( final Exception e ) {
1476                             exception = true;
1477                             exceptionOccuredDuringOpenFile( e );
1478                         }
1479                     }
1480                     else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {
1481                         try {
1482                             final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
1483                             setSpecialOptionsForNexParser( nex );
1484                             phys = PhylogenyMethods.readPhylogenies( nex, file );
1485                             nhx_or_nexus = true;
1486                         }
1487                         catch ( final Exception e ) {
1488                             exception = true;
1489                             exceptionOccuredDuringOpenFile( e );
1490                         }
1491                     }
1492                     // "*.*":
1493                     else {
1494                         try {
1495                             final PhylogenyParser parser = ParserUtils
1496                                     .createParserDependingOnFileType( file,
1497                                                                       getConfiguration()
1498                                                                               .isValidatePhyloXmlAgainstSchema() );
1499                             if ( parser instanceof NexusPhylogeniesParser ) {
1500                                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
1501                                 setSpecialOptionsForNexParser( nex );
1502                                 nhx_or_nexus = true;
1503                             }
1504                             else if ( parser instanceof NHXParser ) {
1505                                 final NHXParser nhx = ( NHXParser ) parser;
1506                                 setSpecialOptionsForNhxParser( nhx );
1507                                 nhx_or_nexus = true;
1508                             }
1509                             else if ( parser instanceof PhyloXmlParser ) {
1510                                 warnIfNotPhyloXmlValidation( getConfiguration() );
1511                             }
1512                             phys = PhylogenyMethods.readPhylogenies( parser, file );
1513                         }
1514                         catch ( final Exception e ) {
1515                             exception = true;
1516                             exceptionOccuredDuringOpenFile( e );
1517                         }
1518                     }
1519                     if ( _mainpanel.getCurrentTreePanel() != null ) {
1520                         _mainpanel.getCurrentTreePanel().setArrowCursor();
1521                     }
1522                     else {
1523                         _mainpanel.setArrowCursor();
1524                     }
1525                     if ( !exception && ( phys != null ) && ( phys.length > 0 ) ) {
1526                         boolean one_desc = false;
1527                         if ( nhx_or_nexus ) {
1528                             for( final Phylogeny phy : phys ) {
1529                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
1530                                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
1531                                 }
1532                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
1533                                     one_desc = true;
1534                                     break;
1535                                 }
1536                             }
1537                         }
1538                         if ( PREPROCESS_TREES ) {
1539                             preProcessTreesUponReading( phys );
1540                         }
1541                         AptxUtil.addPhylogeniesToTabs( phys,
1542                                                        file.getName(),
1543                                                        file.getAbsolutePath(),
1544                                                        getConfiguration(),
1545                                                        getMainPanel() );
1546                         _mainpanel.getControlPanel().showWhole();
1547                         if ( nhx_or_nexus && one_desc ) {
1548                             JOptionPane.showMessageDialog( this,
1549                                                            "One or more trees contain (a) node(s) with one descendant, "
1550                                                                    + ForesterUtil.LINE_SEPARATOR
1551                                                                    + "possibly indicating illegal parentheses within node names.",
1552                                                            "Warning: Possible Error in New Hampshire Formatted Data",
1553                                                            JOptionPane.WARNING_MESSAGE );
1554                         }
1555                     }
1556                 }
1557             }
1558         }
1559         activateSaveAllIfNeeded();
1560         System.gc();
1561     }
1562
1563     private void readSpeciesTreeFromFile() {
1564         Phylogeny t = null;
1565         boolean exception = false;
1566         final File my_dir = getCurrentDir();
1567         _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );
1568         if ( my_dir != null ) {
1569             _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );
1570         }
1571         final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );
1572         final File file = _open_filechooser_for_species_tree.getSelectedFile();
1573         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
1574             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
1575                 try {
1576                     final Phylogeny[] trees = PhylogenyMethods
1577                             .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
1578                     t = trees[ 0 ];
1579                 }
1580                 catch ( final Exception e ) {
1581                     exception = true;
1582                     exceptionOccuredDuringOpenFile( e );
1583                 }
1584             }
1585             else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {
1586                 try {
1587                     final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
1588                     t = trees[ 0 ];
1589                 }
1590                 catch ( final Exception e ) {
1591                     exception = true;
1592                     exceptionOccuredDuringOpenFile( e );
1593                 }
1594             }
1595             // "*.*":
1596             else {
1597                 try {
1598                     final Phylogeny[] trees = PhylogenyMethods
1599                             .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
1600                     t = trees[ 0 ];
1601                 }
1602                 catch ( final Exception e ) {
1603                     exception = true;
1604                     exceptionOccuredDuringOpenFile( e );
1605                 }
1606             }
1607             if ( !exception && ( t != null ) && !t.isRooted() ) {
1608                 exception = true;
1609                 t = null;
1610                 JOptionPane.showMessageDialog( this,
1611                                                "Species tree is not rooted",
1612                                                "Species tree not loaded",
1613                                                JOptionPane.ERROR_MESSAGE );
1614             }
1615             if ( !exception && ( t != null ) ) {
1616                 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
1617                 for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {
1618                     final PhylogenyNode node = it.next();
1619                     if ( !node.getNodeData().isHasTaxonomy() ) {
1620                         exception = true;
1621                         t = null;
1622                         JOptionPane.showMessageDialog( this,
1623                                                        "Species tree contains external node(s) without taxonomy information",
1624                                                        "Species tree not loaded",
1625                                                        JOptionPane.ERROR_MESSAGE );
1626                         break;
1627                     }
1628                     else {
1629                         if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
1630                             exception = true;
1631                             t = null;
1632                             JOptionPane
1633                                     .showMessageDialog( this,
1634                                                         "Taxonomy [" + node.getNodeData().getTaxonomy().asSimpleText()
1635                                                                 + "] is not unique in species tree",
1636                                                         "Species tree not loaded",
1637                                                         JOptionPane.ERROR_MESSAGE );
1638                             break;
1639                         }
1640                         else {
1641                             tax_set.add( node.getNodeData().getTaxonomy() );
1642                         }
1643                     }
1644                 }
1645             }
1646             if ( !exception && ( t != null ) ) {
1647                 setSpeciesTree( t );
1648                 JOptionPane.showMessageDialog( this,
1649                                                "Species tree successfully loaded",
1650                                                "Species tree loaded",
1651                                                JOptionPane.INFORMATION_MESSAGE );
1652             }
1653             _contentpane.repaint();
1654             System.gc();
1655         }
1656     }
1657
1658     private void setArrowCursor() {
1659         try {
1660             _mainpanel.getCurrentTreePanel().setArrowCursor();
1661         }
1662         catch ( final Exception ex ) {
1663             // Do nothing.
1664         }
1665     }
1666
1667     private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {
1668         _min_not_collapse_bl = min_not_collapse_bl;
1669     }
1670
1671     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {
1672         _min_not_collapse = min_not_collapse;
1673     }
1674
1675     private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {
1676         _phylogenetic_inference_options = phylogenetic_inference_options;
1677     }
1678
1679     private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {
1680         nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
1681         nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
1682         nex.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
1683     }
1684
1685     private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
1686         nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
1687         nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );
1688         nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );
1689         nhx.setParseBeastStyleExtendedTags( getOptions().isParseBeastStyleExtendedNexusTags() );
1690     }
1691
1692     void buildAnalysisMenu() {
1693         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
1694         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
1695         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
1696         _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
1697         customizeJMenuItem( _gsdi_item );
1698         customizeJMenuItem( _gsdir_item );
1699         customizeJMenuItem( _load_species_tree_item );
1700         _analysis_menu.addSeparator();
1701         _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
1702         customizeJMenuItem( _lineage_inference );
1703         _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
1704         _jmenubar.add( _analysis_menu );
1705     }
1706
1707     @Override
1708     void buildFileMenu() {
1709         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
1710         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
1711         _file_jmenu.addSeparator();
1712         _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
1713         _file_jmenu.addSeparator();
1714         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
1715         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
1716                 .getAvailablePhylogeniesWebserviceClients().size() ];
1717         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
1718             final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
1719             _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
1720             _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );
1721         }
1722         if ( getConfiguration().isEditable() ) {
1723             _file_jmenu.addSeparator();
1724             _file_jmenu.add( _new_item = new JMenuItem( "New" ) );
1725             _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );
1726         }
1727         _file_jmenu.addSeparator();
1728         _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
1729         _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );
1730         _save_all_item.setToolTipText( "Write all phylogenies to one file." );
1731         _save_all_item.setEnabled( false );
1732         _file_jmenu.addSeparator();
1733         _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
1734         if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" )
1735                 || AptxUtil.canWriteFormat( "TIF" ) ) {
1736             _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
1737         }
1738         _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
1739         _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
1740         if ( AptxUtil.canWriteFormat( "gif" ) ) {
1741             _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
1742         }
1743         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
1744             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
1745         }
1746         _file_jmenu.addSeparator();
1747         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
1748         _file_jmenu.addSeparator();
1749         _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );
1750         _close_item.setToolTipText( "To close the current pane." );
1751         _close_item.setEnabled( true );
1752         _file_jmenu.addSeparator();
1753         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
1754         customizeJMenuItem( _open_item );
1755         _open_item.setFont( new Font( _open_item.getFont().getFontName(),
1756                                       Font.BOLD,
1757                                       _open_item.getFont().getSize() + 4 ) );
1758         customizeJMenuItem( _open_url_item );
1759         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
1760             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
1761         }
1762         customizeJMenuItem( _save_item );
1763         if ( getConfiguration().isEditable() ) {
1764             customizeJMenuItem( _new_item );
1765         }
1766         customizeJMenuItem( _close_item );
1767         customizeJMenuItem( _save_all_item );
1768         customizeJMenuItem( _write_to_pdf_item );
1769         customizeJMenuItem( _write_to_png_item );
1770         customizeJMenuItem( _write_to_jpg_item );
1771         customizeJMenuItem( _write_to_gif_item );
1772         customizeJMenuItem( _write_to_tif_item );
1773         customizeJMenuItem( _write_to_bmp_item );
1774         customizeJMenuItem( _print_item );
1775         customizeJMenuItem( _exit_item );
1776         _jmenubar.add( _file_jmenu );
1777     }
1778
1779     void buildOptionsMenu() {
1780         _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
1781         _options_jmenu.addChangeListener( new ChangeListener() {
1782
1783             @Override
1784             public void stateChanged( final ChangeEvent e ) {
1785                 MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
1786                 MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
1787                 MainFrame.setTextMinSupportMenuItem( _choose_minimal_confidence_mi,
1788                                                      getOptions(),
1789                                                      getCurrentTreePanel() );
1790                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi,
1791                                                          MainFrame.createCurrentFontDesc( getMainPanel()
1792                                                                  .getTreeFontSet() ) );
1793                 //  MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
1794                 MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
1795                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
1796                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
1797                 MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
1798                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
1799                 try {
1800                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
1801                     getMainPanel().getControlPanel().setVisibilityOfX();
1802                 }
1803                 catch ( final Exception ignore ) {
1804                     // do nothing, not important.
1805                 }
1806             }
1807         } );
1808         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
1809         _options_jmenu
1810                 .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
1811         _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
1812         _radio_group_1 = new ButtonGroup();
1813         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
1814          _radio_group_1.add( _non_lined_up_cladograms_rbmi );
1815         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
1816         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
1817         _options_jmenu
1818                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
1819         _options_jmenu
1820                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
1821         _options_jmenu
1822                 .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
1823
1824         _options_jmenu
1825         .add( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) );
1826
1827
1828         _options_jmenu
1829         .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) );
1830
1831
1832
1833         _options_jmenu
1834                 .add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
1835
1836
1837
1838         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
1839             _options_jmenu
1840                     .add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
1841             _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
1842         }
1843         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
1844         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
1845         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
1846         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
1847         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
1848         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
1849         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
1850         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
1851         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
1852         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
1853         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
1854         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
1855         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
1856         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
1857         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
1858         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
1859         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
1860         _options_jmenu.addSeparator();
1861         _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
1862         _options_jmenu.addSeparator();
1863         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
1864         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
1865         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
1866         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
1867         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
1868         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
1869         _options_jmenu
1870                 .add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
1871         _options_jmenu.addSeparator();
1872         _options_jmenu
1873                 .add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), getConfiguration() ) );
1874         _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
1875         _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
1876         _options_jmenu
1877                 .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
1878         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
1879         _options_jmenu.addSeparator();
1880         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
1881         _options_jmenu
1882                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
1883         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
1884         _options_jmenu
1885                 .add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
1886         _parse_beast_style_extended_nexus_tags_cbmi
1887                 .setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
1888         _options_jmenu
1889                 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
1890         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
1891         _options_jmenu
1892                 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
1893         _options_jmenu
1894                 .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
1895         _options_jmenu
1896                 .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
1897         _extract_taxonomy_pfam_strict_rbmi
1898                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
1899         _extract_taxonomy_pfam_relaxed_rbmi
1900                 .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
1901         _extract_taxonomy_agressive_rbmi
1902                 .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
1903         _radio_group_2 = new ButtonGroup();
1904         _radio_group_2.add( _extract_taxonomy_no_rbmi );
1905         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
1906         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
1907         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
1908         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
1909         _options_jmenu
1910                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
1911         _use_brackets_for_conf_in_nh_export_cbmi
1912                 .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
1913         _options_jmenu
1914                 .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
1915         customizeJMenuItem( _choose_font_mi );
1916         customizeJMenuItem( _choose_minimal_confidence_mi );
1917         customizeJMenuItem( _switch_colors_mi );
1918         customizeJMenuItem( _choose_pdf_width_mi );
1919         customizeJMenuItem( _overview_placment_mi );
1920         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi,
1921                                    getOptions().isShowDefaultNodeShapesExternal() );
1922         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi,
1923                                    getOptions().isShowDefaultNodeShapesInternal() );
1924         customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi,
1925                                    getOptions().isShowDefaultNodeShapesForMarkedNodes() );
1926         customizeJMenuItem( _cycle_node_shape_mi );
1927         customizeJMenuItem( _cycle_node_fill_mi );
1928         customizeJMenuItem( _choose_node_size_mi );
1929         customizeJMenuItem( _cycle_data_return );
1930         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch,
1931                                    getOptions().isColorLabelsSameAsParentBranch() );
1932         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
1933         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
1934         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
1935         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
1936         customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
1937         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
1938         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
1939         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
1940         customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
1941         customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() );
1942
1943         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
1944                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
1945         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
1946                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
1947         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
1948         customizeCheckBoxMenuItem( _label_direction_cbmi,
1949                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
1950         customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
1951         customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
1952         customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi,
1953                                    getOptions().isInternalNumberAreConfidenceForNhParsing() );
1954         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
1955                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
1956         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
1957                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
1958         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
1959                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
1960         customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
1961                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
1962         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
1963         customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi,
1964                                    getOptions().isReplaceUnderscoresInNhParsing() );
1965         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
1966         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
1967         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
1968         customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi,
1969                                    getOptions().isColorAllFoundNodesWhenColoringSubtree() );
1970         customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi,
1971                                    getOptions().isParseBeastStyleExtendedNexusTags() );
1972         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
1973         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
1974         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi,
1975                                    getOptions()
1976                                            .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
1977         customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi,
1978                                    getOptions()
1979                                            .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
1980         customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
1981         customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
1982         _jmenubar.add( _options_jmenu );
1983     }
1984
1985     void buildPhylogeneticInferenceMenu() {
1986         final InferenceManager im = getInferenceManager();
1987         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
1988         _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
1989         customizeJMenuItem( _inference_from_msa_item );
1990         _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
1991         if ( im.canDoMsa() ) {
1992             _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
1993             customizeJMenuItem( _inference_from_seqs_item );
1994             _inference_from_seqs_item
1995                     .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
1996         }
1997         else {
1998             _inference_menu
1999                     .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
2000             customizeJMenuItem( _inference_from_seqs_item );
2001             _inference_from_seqs_item.setEnabled( false );
2002         }
2003         _jmenubar.add( _inference_menu );
2004     }
2005
2006     void buildToolsMenu() {
2007         _tools_menu = createMenu( "Tools", getConfiguration() );
2008         _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
2009         customizeJMenuItem( _confcolor_item );
2010         _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
2011         customizeJMenuItem( _color_rank_jmi );
2012         _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
2013         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
2014         customizeJMenuItem( _taxcolor_item );
2015         _tools_menu.addSeparator();
2016         _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
2017         _remove_visual_styles_item
2018                 .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
2019         customizeJMenuItem( _remove_visual_styles_item );
2020         _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
2021         _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
2022         customizeJMenuItem( _remove_branch_color_item );
2023         _tools_menu.addSeparator();
2024         _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
2025         customizeJMenuItem( _annotate_item );
2026         _tools_menu.addSeparator();
2027         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
2028         customizeJMenuItem( _midpoint_root_item );
2029         _tools_menu.addSeparator();
2030         _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );
2031         _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );
2032         customizeJMenuItem( _delete_selected_nodes_item );
2033         _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );
2034         _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
2035         customizeJMenuItem( _delete_not_selected_nodes_item );
2036         _tools_menu.addSeparator();
2037         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Single Taxonomy-Subtrees" ) );
2038         customizeJMenuItem( _collapse_species_specific_subtrees );
2039         _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as species specific subtrees)" );
2040         _tools_menu
2041                 .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
2042         customizeJMenuItem( _collapse_below_threshold );
2043         _collapse_below_threshold
2044                 .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
2045         //
2046         _tools_menu
2047                 .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
2048         customizeJMenuItem( _collapse_below_branch_length );
2049         _collapse_below_branch_length
2050                 .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
2051         //
2052         _tools_menu.addSeparator();
2053         _tools_menu
2054                 .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
2055         customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
2056         _extract_tax_code_from_node_names_jmi
2057                 .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
2058         _tools_menu
2059                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
2060         customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
2061         _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
2062         _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
2063         customizeJMenuItem( _move_node_names_to_seq_names_jmi );
2064         _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );
2065         _tools_menu.addSeparator();
2066         _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
2067         customizeJMenuItem( _obtain_seq_information_jmi );
2068         _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
2069         _tools_menu
2070                 .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
2071         customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
2072         _obtain_detailed_taxonomic_information_jmi
2073                 .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
2074         _tools_menu
2075                 .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
2076         customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
2077         _obtain_detailed_taxonomic_information_deleting_jmi
2078                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
2079         _tools_menu.addSeparator();
2080         _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
2081         customizeJMenuItem( _read_values_jmi );
2082         _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );
2083         _jmenubar.add( _tools_menu );
2084         _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
2085         customizeJMenuItem( _read_seqs_jmi );
2086         _read_seqs_jmi
2087                 .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
2088         _jmenubar.add( _tools_menu );
2089     }
2090
2091     @Override
2092     void close() {
2093         if ( isUnsavedDataPresent() ) {
2094             final int r = JOptionPane.showConfirmDialog( this,
2095                                                          "Exit despite potentially unsaved changes?",
2096                                                          "Exit?",
2097                                                          JOptionPane.YES_NO_OPTION );
2098             if ( r != JOptionPane.YES_OPTION ) {
2099                 return;
2100             }
2101         }
2102         exit();
2103     }
2104
2105     void exit() {
2106         removeAllTextFrames();
2107         _mainpanel.terminate();
2108         _contentpane.removeAll();
2109         setVisible( false );
2110         dispose();
2111         // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.
2112     }
2113
2114     void readPhylogeniesFromURL() {
2115         URL url = null;
2116         Phylogeny[] phys = null;
2117         final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
2118         final String url_string = JOptionPane
2119                 .showInputDialog( this,
2120                                   message,
2121                                   "Use URL/webservice to obtain a phylogeny",
2122                                   JOptionPane.QUESTION_MESSAGE );
2123         boolean nhx_or_nexus = false;
2124         if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
2125             try {
2126                 url = new URL( url_string );
2127                 PhylogenyParser parser = null;
2128                 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
2129                     parser = new TolParser();
2130                 }
2131                 else {
2132                     parser = ParserUtils
2133                             .createParserDependingOnUrlContents( url,
2134                                                                  getConfiguration().isValidatePhyloXmlAgainstSchema() );
2135                 }
2136                 if ( parser instanceof NexusPhylogeniesParser ) {
2137                     nhx_or_nexus = true;
2138                 }
2139                 else if ( parser instanceof NHXParser ) {
2140                     nhx_or_nexus = true;
2141                 }
2142                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2143                     _mainpanel.getCurrentTreePanel().setWaitCursor();
2144                 }
2145                 else {
2146                     _mainpanel.setWaitCursor();
2147                 }
2148                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
2149                 phys = factory.create( url.openStream(), parser );
2150             }
2151             catch ( final MalformedURLException e ) {
2152                 JOptionPane.showMessageDialog( this,
2153                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
2154                                                "Malformed URL",
2155                                                JOptionPane.ERROR_MESSAGE );
2156             }
2157             catch ( final IOException e ) {
2158                 JOptionPane.showMessageDialog( this,
2159                                                "Could not read from " + url + "\n"
2160                                                        + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2161                                                "Failed to read URL",
2162                                                JOptionPane.ERROR_MESSAGE );
2163             }
2164             catch ( final Exception e ) {
2165                 JOptionPane.showMessageDialog( this,
2166                                                ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
2167                                                "Unexpected Exception",
2168                                                JOptionPane.ERROR_MESSAGE );
2169             }
2170             finally {
2171                 if ( _mainpanel.getCurrentTreePanel() != null ) {
2172                     _mainpanel.getCurrentTreePanel().setArrowCursor();
2173                 }
2174                 else {
2175                     _mainpanel.setArrowCursor();
2176                 }
2177             }
2178             if ( ( phys != null ) && ( phys.length > 0 ) ) {
2179                 if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
2180                     for( final Phylogeny phy : phys ) {
2181                         PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
2182                     }
2183                 }
2184                 AptxUtil.addPhylogeniesToTabs( phys,
2185                                                new File( url.getFile() ).getName(),
2186                                                new File( url.getFile() ).toString(),
2187                                                getConfiguration(),
2188                                                getMainPanel() );
2189                 _mainpanel.getControlPanel().showWhole();
2190             }
2191         }
2192         activateSaveAllIfNeeded();
2193         System.gc();
2194     }
2195
2196     void setMsa( final Msa msa ) {
2197         _msa = msa;
2198     }
2199
2200     void setMsaFile( final File msa_file ) {
2201         _msa_file = msa_file;
2202     }
2203
2204     void setSeqs( final List<MolecularSequence> seqs ) {
2205         _seqs = seqs;
2206     }
2207
2208     void setSeqsFile( final File seqs_file ) {
2209         _seqs_file = seqs_file;
2210     }
2211
2212     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
2213         return new MainFrameApplication( phys, config );
2214     }
2215
2216     public static MainFrame createInstance( final Phylogeny[] phys,
2217                                             final Configuration config,
2218                                             final String title,
2219                                             final File current_dir ) {
2220         return new MainFrameApplication( phys, config, title, current_dir );
2221     }
2222
2223     static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {
2224         return new MainFrameApplication( phys, config, title );
2225     }
2226
2227     static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
2228         return new MainFrameApplication( phys, config_file_name, title );
2229     }
2230
2231     static void warnIfNotPhyloXmlValidation( final Configuration c ) {
2232         if ( !c.isValidatePhyloXmlAgainstSchema() ) {
2233             JOptionPane.showMessageDialog( null,
2234                                            ForesterUtil.wordWrap(
2235                                                                   "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
2236                                                                   80 ),
2237                                            "Warning",
2238                                            JOptionPane.WARNING_MESSAGE );
2239         }
2240     }
2241 } // MainFrameApplication.